open-computational-neuroscience-resources
github.com/asoplata/open-computational-neuroscience-resources ↗A publicly-editable collection of open computational neuroscience resources
Use this list with your AI agent
Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:
"Show me simulation software resources from open-computational-neuroscience-resources"
Installation instructions →What's inside
Open Data
- 3D Brain Atlas Reconstructor
- 3DModelDB - A collection of 3D printable versions of published neuron
morphologies, both traced and
artificial.
A collection of 3D printable versions of published neuron morphologies, both traced and artificial.
- Allen Brain Atlas Data Portal
How to programmatically download and use Allen data
- AllenSDK - How to programmatically download and use Allen data
How to programmatically download and use Allen data
- BioModels - Not neuroscience-specific
Not neuroscience-specific
- BODB - Brain Operation Database System
Brain Operation Database System
Meta-resources
- Allen Institute for Brain Science
- COMBINE - Computational modeling in biology network
Computational modeling in biology network
- Comparison of Neural Network Simulators
- Computational Neuroscience journals
- "Computational Neuroscience on the Web" (Jim Perlewitz) - Probably the most
comprehensive curated list of computational neuroscience modeling tools on
the internet. HIGHLY recommended.
Probably the most comprehensive
- "Computational Neuroscience Resources" (Dan Goodman)
Reproducibility and Provenance
- Alpaca - Provenance for data analysis in Python
Provenance for data analysis in Python
- Neo
- Snakemake - Scalable, reproducible workflows using a Python-like language
Scalable, reproducible workflows using a Python-like language
Organizations and Communities
- An Open Computational Neuroscience list I've made on Twitter
- CodeNeuro - Bringing neuroscience and data science together
Bringing neuroscience and data science together
- Funding research software developmentFunding
- G-NODE - German Informatics Node
German Informatics Node
- INCF - International Neuroinformatics Coordinating
Facility
International Neuroinformatics Coordinating Facility
- NeuralEnsemble, focused on software development in neuroscience
Open Code
- Arbor - High-performance library for computational neuroscience simulationsSimulation Software
High-performance library for computational neuroscience simulations
- bctnet - Brain Connectivity Toolbox for complex-network analysisAnalysis Software
Brain Connectivity Toolbox for complex-network analysis
- BindsNET - Simulation of spiking neural networks (SNNs) using PyTorchSimulation Software
Simulation of spiking neural networks (SNNs) using PyTorch
- BluePyOpt - Blue Brain Python Optimisation Library, for optimizing parameters in neural modelsSimulation Software
Blue Brain Python Optimisation Library, for optimizing parameters in neural models
- BRAHMS - A modular execution framework for executing integrated systems built from component software processesSimulation Software
A modular execution framework for executing integrated systems built from component software processes
- Brain Dynamics Toolbox - Open software for simulating dynamical systems in neuroscience using MATLABSimulation Software
Open software for simulating dynamical systems in neuroscience using MATLAB
Specification of Model and Data Markup Languages
- CellML - A model specification language for general biological mathematical
modeling
A model specification language for general biological mathematical modeling
- https://docs.neuroml.org/Userdocs/Software/SupportingTools.html
- NESTML - Domain-specific language for neuron models and code generation
toolchain
Domain-specific language for neuron models and code generation toolchain
- NeuroML - A model description language for computational
neuroscience
A model description language for computational neuroscience
- NineML - A model specification language for
neuroscience
A model specification language for neuroscience
- SpineML - A declarative XML-based model description language for large scale neural network models
A declarative XML-based model description language for large scale neural network models
Open Courses and Educational Resources
- Course: Computational Neuroscience at Coursera
- Course: Computational Neuroscience: Neuronal Dynamics of Cognition at edX
- Course/Curriculum: Mathematical Tools for Neuroscientists
- Course: Introduction To Modern Brain-Computer Interface Design
- Course: Neuronal Dynamics at edX
- Course: Simulation Neuroscience at edX
Showing a sample of 173 resources. View the full list on GitHub →